From 16S rRNA-gene sequencing of cow SWAB microbiome samples: - 3 timepoints (T0 BEFORE, T0 AFTER AND T8) for SWAB samples and two treatments (oil, treated/untreated)
Between-sample variability from 16S rRna-gene sequencing data.
Clustering by timepoint (PCA):
Clustering by treatment (PCA): after removing samples from timepoint 0 # BECAUSE WE KNOW THAT AT TIMEPOINT 0 WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS
Clustering by type (MDS): NMDS2 vs NMDS3
## Warning in metaMDS(matx): stress is (nearly) zero: you may have insufficient
## data
Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.
Below the ANOVA table from the model:
\[ X = \mu + treatment + timepoint + treatment*type + e \]
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| treatment | 1 | 0.1439951 | 0.1439951 | 1.316741 | 0.0417820 | 0.111 |
| timepoint | 1 | 0.1309875 | 0.1309875 | 1.197795 | 0.0380077 | 0.210 |
| residuals | 29 | 3.1713598 | 0.1093572 | NA | 0.9202103 | NA |
| total | 31 | 3.4463424 | NA | NA | 1.0000000 | NA |
## Run 0 stress 0.000149963
## Run 1 stress 9.97299e-05
## ... New best solution
## ... Procrustes: rmse 0.0001014245 max resid 0.0002806771
## ... Similar to previous best
## Run 2 stress 9.883956e-05
## ... New best solution
## ... Procrustes: rmse 4.618237e-05 max resid 0.000195706
## ... Similar to previous best
## Run 3 stress 9.672124e-05
## ... New best solution
## ... Procrustes: rmse 4.426533e-05 max resid 0.0001897678
## ... Similar to previous best
## Run 4 stress 0.00011099
## ... Procrustes: rmse 3.122843e-05 max resid 8.742987e-05
## ... Similar to previous best
## Run 5 stress 9.355347e-05
## ... New best solution
## ... Procrustes: rmse 0.0001013662 max resid 0.0003823866
## ... Similar to previous best
## Run 6 stress 9.775024e-05
## ... Procrustes: rmse 8.320419e-05 max resid 0.0002145534
## ... Similar to previous best
## Run 7 stress 0.0001252052
## ... Procrustes: rmse 0.0001231785 max resid 0.0004204665
## ... Similar to previous best
## Run 8 stress 9.677272e-05
## ... Procrustes: rmse 6.000703e-05 max resid 0.0001955693
## ... Similar to previous best
## Run 9 stress 9.833002e-05
## ... Procrustes: rmse 5.248124e-05 max resid 0.0001764376
## ... Similar to previous best
## Run 10 stress 9.95221e-05
## ... Procrustes: rmse 0.0001085135 max resid 0.0003993056
## ... Similar to previous best
## Run 11 stress 9.569179e-05
## ... Procrustes: rmse 0.000100508 max resid 0.0004735585
## ... Similar to previous best
## Run 12 stress 9.77646e-05
## ... Procrustes: rmse 9.442084e-05 max resid 0.0003447424
## ... Similar to previous best
## Run 13 stress 9.969321e-05
## ... Procrustes: rmse 0.0001275208 max resid 0.0004873466
## ... Similar to previous best
## Run 14 stress 8.961434e-05
## ... New best solution
## ... Procrustes: rmse 0.0001146834 max resid 0.000545623
## ... Similar to previous best
## Run 15 stress 9.88076e-05
## ... Procrustes: rmse 0.000164074 max resid 0.0006564917
## ... Similar to previous best
## Run 16 stress 9.625181e-05
## ... Procrustes: rmse 0.000159187 max resid 0.0006445011
## ... Similar to previous best
## Run 17 stress 9.739688e-05
## ... Procrustes: rmse 0.0001108413 max resid 0.0004631666
## ... Similar to previous best
## Run 18 stress 9.684643e-05
## ... Procrustes: rmse 0.0001240389 max resid 0.0003018623
## ... Similar to previous best
## Run 19 stress 9.712024e-05
## ... Procrustes: rmse 0.0001625145 max resid 0.0006541186
## ... Similar to previous best
## Run 20 stress 9.962206e-05
## ... Procrustes: rmse 0.0001514454 max resid 0.0005570829
## ... Similar to previous best
## *** Solution reached